Reichu wrote:1. What was Nono doing in a comet?
I don't think we're told specifically, but I have a feeling it has something to do with the "fabled ruins" they mentioned in passing during episode 6 that was one of the old spaceships from the first Gunbuster. Something made her shut down, or go into sleep mode, and dust and shit accumulated around her over a couple thousand years.
Reichu wrote:2. Why the heck do they call the real space monsters "variable gravity wells"?
Because the only true space monster they've seen so far was the one on Titan, which kept fluctuating the gravity of the moon. Since they were the same kind of creature, they just called the one from the Black Hole Exelio a Fluctuating Gravity Well as well. Keep in mind though, they were still calling the Buster Legion "Space monsters", so that was already taken.
Reichu wrote:3. Why was the Exelio black hole termed the new 11th planet?
Because it's cool. It probably orbited the system like a planet.
Reichu wrote:4. Why did it take the Exelio space monster six months to reach Earth after warping?
Needed time to evolve to it's 3rd evolutionary stage? I think this had something to do with the Rip Van Winkle effect. See the note about science in the next answer.
Reichu wrote:5. How the heck did an uber-space monster end up assimilating the black hole, anyway?
Probably has something to do with the true space monsters' ability to fluctuate the gravity around them. Keep in mind, Gunbuster 2's rubber science is even more flexible than Gunbuster's.
Reichu wrote:6. How come a planet-sized ultimate humanoid weapon gets totally pwnd by 3-eyes, but "Nana-gou" Nono and Topless-less Oneesama in the restored Dix-Neuf can effortlessly defeat the thing with Inazuma Double Kick and the power of Sisterly Love? (And I won't accept "hard work and guts" for an answer.

)
Sorry, but the answer is given in the show by Lal'C, and the answer IS "Hard work and guts".
Reichu wrote:7. Exactly what is Nono's "singularity"? (Yeah, I know it has something to do with the physics of black holes.)
Nono is speaking metaphorically. She means that she wants Lal'C to know that Nono truly cares for her. It's her feelings for Lal'C. Basically, it's a paper crane.
Reichu wrote:8. WTF happened to Nono, exactly?
From pg. 16 of vol. 3's booklet:
Interviewer: The cosmic censor scene was powerful.
Tsurumaki: We visually depicted the cosmic censorship hypothesis. (laughs) The content described appears to be like Nono's wish, and as it is told as though real, it can also appear as if Nono may have already experienced this. Nono vanishes beyond the gravitational singularity and goes beyond time. Thus, in the near future, or the far, far future, Nono and Lal'C may go see the skylarks together.
"...I follow you both online and offline, and I am a 4-dimensional manifestation of absolute evil..." - Reichu-tachi
"In all cases, eventually it becomes necessary to decide to 'deliberately betray the fans.'" - Yoji Enokido
I believe in the director of Eva 1.11.